Starting phenix.real_space_refine on Thu Feb 15 10:20:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2024/6tmh_10521_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2024/6tmh_10521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2024/6tmh_10521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2024/6tmh_10521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2024/6tmh_10521_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2024/6tmh_10521_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 166 5.16 5 C 20479 2.51 5 N 5547 2.21 5 O 6200 1.98 5 H 32948 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "i ASP 62": "OD1" <-> "OD2" Residue "i TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ASP 77": "OD1" <-> "OD2" Residue "i TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 129": "OD1" <-> "OD2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C ASP 385": "OD1" <-> "OD2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 463": "OD1" <-> "OD2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B ARG 435": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 473": "OD1" <-> "OD2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B ASP 479": "OD1" <-> "OD2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 196": "OD1" <-> "OD2" Residue "F PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 367": "OD1" <-> "OD2" Residue "F TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 473": "OD1" <-> "OD2" Residue "F ASP 479": "OD1" <-> "OD2" Residue "F PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 473": "OD1" <-> "OD2" Residue "D GLU 474": "OE1" <-> "OE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 169": "OE1" <-> "OE2" Residue "g PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 237": "OE1" <-> "OE2" Residue "d TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ASP 101": "OD1" <-> "OD2" Residue "d PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ASP 120": "OD1" <-> "OD2" Residue "d ASP 121": "OD1" <-> "OD2" Residue "d GLU 162": "OE1" <-> "OE2" Residue "e GLU 26": "OE1" <-> "OE2" Residue "e GLU 42": "OE1" <-> "OE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 109": "OD1" <-> "OD2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 137": "OD1" <-> "OD2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 136": "OE1" <-> "OE2" Residue "O TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 65358 Number of models: 1 Model: "" Number of chains: 26 Chain: "i" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 660 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 2, 'TRANS': 37} Chain: "A" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7924 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 490} Chain: "E" Number of atoms: 7848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7848 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 486} Chain: "C" Number of atoms: 7521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7521 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466} Chain: "B" Number of atoms: 7314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 7314 Classifications: {'peptide': 479} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 454} Chain: "F" Number of atoms: 7265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7265 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 450} Chain: "D" Number of atoms: 7265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7265 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 450} Chain: "g" Number of atoms: 4289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4289 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain: "d" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2145 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "e" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1077 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "G" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1618 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain breaks: 1 Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "I" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "J" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "K" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "L" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "M" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "N" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "O" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "P" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "Q" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.72, per 1000 atoms: 0.33 Number of scatterers: 65358 At special positions: 0 Unit cell: (135.29, 126.99, 229.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 166 16.00 P 13 15.00 Mg 5 11.99 O 6200 8.00 N 5547 7.00 C 20479 6.00 H 32948 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.77 Conformation dependent library (CDL) restraints added in 5.5 seconds 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 149 helices and 25 sheets defined 49.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.14 Creating SS restraints... Processing helix chain 'i' and resid 58 through 87 removed outlier: 4.883A pdb=" N LEU i 85 " --> pdb=" O LEU i 81 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALA i 86 " --> pdb=" O ARG i 82 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN i 87 " --> pdb=" O ASN i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 95 No H-bonds generated for 'chain 'i' and resid 93 through 95' Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 63 through 66 No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 226 through 242 removed outlier: 4.131A pdb=" N GLN A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 4.357A pdb=" N GLN A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 292 through 312 Proline residue: A 299 - end of helix removed outlier: 3.821A pdb=" N TRP A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE A 309 " --> pdb=" O MET A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 350 through 360 removed outlier: 4.258A pdb=" N ARG A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 407 through 410 No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 427 through 430 Processing helix chain 'A' and resid 433 through 451 removed outlier: 4.277A pdb=" N VAL A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 457 removed outlier: 3.749A pdb=" N GLN A 457 " --> pdb=" O ALA A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 467 through 480 Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 510 through 527 removed outlier: 4.251A pdb=" N SER A 514 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 517 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 538 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 226 through 242 removed outlier: 4.163A pdb=" N GLN E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE E 240 " --> pdb=" O ASN E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 274 Processing helix chain 'E' and resid 292 through 312 Proline residue: E 299 - end of helix removed outlier: 3.822A pdb=" N TRP E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE E 309 " --> pdb=" O MET E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 350 through 358 Processing helix chain 'E' and resid 389 through 395 Processing helix chain 'E' and resid 406 through 411 Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 433 through 455 removed outlier: 3.902A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA E 454 " --> pdb=" O ARG E 450 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE E 455 " --> pdb=" O GLU E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 479 Processing helix chain 'E' and resid 490 through 502 Processing helix chain 'E' and resid 511 through 524 removed outlier: 3.678A pdb=" N SER E 514 " --> pdb=" O LYS E 511 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 516 " --> pdb=" O ILE E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 538 Processing helix chain 'E' and resid 543 through 559 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 226 through 242 removed outlier: 4.180A pdb=" N GLN C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE C 240 " --> pdb=" O ASN C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 removed outlier: 3.760A pdb=" N ARG C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 Proline residue: C 299 - end of helix removed outlier: 3.750A pdb=" N TRP C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE C 309 " --> pdb=" O MET C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 389 through 396 Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 427 through 430 Processing helix chain 'C' and resid 433 through 458 removed outlier: 3.998A pdb=" N VAL C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'C' and resid 490 through 501 Processing helix chain 'C' and resid 510 through 526 removed outlier: 4.055A pdb=" N SER C 514 " --> pdb=" O LYS C 511 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU C 517 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 519 " --> pdb=" O PHE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 538 Processing helix chain 'C' and resid 543 through 559 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 261 through 273 Processing helix chain 'B' and resid 307 through 324 removed outlier: 4.510A pdb=" N ALA B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.618A pdb=" N GLY B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 374 removed outlier: 3.761A pdb=" N LEU B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 399 through 407 removed outlier: 4.291A pdb=" N ALA B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS B 407 " --> pdb=" O THR B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.021A pdb=" N LEU B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 462 removed outlier: 3.672A pdb=" N THR B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 477 through 493 Processing helix chain 'B' and resid 499 through 504 removed outlier: 4.136A pdb=" N VAL B 502 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 504 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 525 Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 542 through 555 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'F' and resid 233 through 246 Processing helix chain 'F' and resid 261 through 274 Processing helix chain 'F' and resid 312 through 324 removed outlier: 3.795A pdb=" N PHE F 322 " --> pdb=" O VAL F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 Processing helix chain 'F' and resid 364 through 372 Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 399 through 404 Processing helix chain 'F' and resid 416 through 419 No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'F' and resid 443 through 470 removed outlier: 3.768A pdb=" N TYR F 447 " --> pdb=" O GLY F 443 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP F 448 " --> pdb=" O GLN F 444 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE F 469 " --> pdb=" O ASP F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 492 Processing helix chain 'F' and resid 500 through 504 Processing helix chain 'F' and resid 513 through 525 Processing helix chain 'F' and resid 542 through 552 Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 261 through 274 Processing helix chain 'D' and resid 311 through 324 removed outlier: 3.771A pdb=" N PHE D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 351 removed outlier: 3.583A pdb=" N GLY D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.918A pdb=" N LEU D 371 " --> pdb=" O ASP D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 399 through 407 removed outlier: 4.154A pdb=" N ALA D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS D 407 " --> pdb=" O THR D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 444 through 469 removed outlier: 3.768A pdb=" N LEU D 463 " --> pdb=" O ASP D 459 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN D 464 " --> pdb=" O TYR D 460 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP D 465 " --> pdb=" O LYS D 461 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 477 through 492 Processing helix chain 'D' and resid 499 through 504 removed outlier: 4.059A pdb=" N VAL D 502 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR D 504 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 525 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'g' and resid 44 through 81 Processing helix chain 'g' and resid 83 through 93 Proline residue: g 87 - end of helix Processing helix chain 'g' and resid 120 through 135 Processing helix chain 'g' and resid 149 through 159 removed outlier: 5.376A pdb=" N ARG g 157 " --> pdb=" O SER g 153 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N THR g 158 " --> pdb=" O ALA g 154 " (cutoff:3.500A) Processing helix chain 'g' and resid 177 through 189 removed outlier: 3.543A pdb=" N ILE g 182 " --> pdb=" O GLY g 178 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE g 183 " --> pdb=" O GLN g 179 " (cutoff:3.500A) Processing helix chain 'g' and resid 218 through 222 Processing helix chain 'g' and resid 227 through 229 No H-bonds generated for 'chain 'g' and resid 227 through 229' Processing helix chain 'g' and resid 238 through 311 removed outlier: 4.959A pdb=" N LYS g 243 " --> pdb=" O THR g 239 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP g 244 " --> pdb=" O ASP g 240 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 139 No H-bonds generated for 'chain 'd' and resid 137 through 139' Processing helix chain 'd' and resid 143 through 156 Processing helix chain 'd' and resid 162 through 181 Processing helix chain 'e' and resid 9 through 23 removed outlier: 3.691A pdb=" N LEU e 19 " --> pdb=" O GLU e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 26 through 34 removed outlier: 3.944A pdb=" N GLN e 31 " --> pdb=" O PRO e 27 " (cutoff:3.500A) Processing helix chain 'e' and resid 59 through 64 Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 94 through 110 Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 124 through 136 Processing helix chain 'G' and resid 142 through 153 Processing helix chain 'G' and resid 157 through 169 removed outlier: 4.239A pdb=" N ALA G 161 " --> pdb=" O PRO G 158 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG G 162 " --> pdb=" O MET G 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 107 Processing helix chain 'H' and resid 110 through 130 Processing helix chain 'H' and resid 132 through 165 removed outlier: 4.994A pdb=" N GLU H 136 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE H 139 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR H 141 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU H 143 " --> pdb=" O THR H 140 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU H 150 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N MET H 159 " --> pdb=" O CYS H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 130 removed outlier: 3.700A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER I 109 " --> pdb=" O ILE I 105 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL I 110 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY I 112 " --> pdb=" O MET I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 163 removed outlier: 5.261A pdb=" N GLU I 136 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE I 139 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU I 150 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 130 removed outlier: 4.381A pdb=" N SER J 109 " --> pdb=" O ILE J 105 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLY J 111 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLY J 112 " --> pdb=" O MET J 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL J 113 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 164 removed outlier: 5.541A pdb=" N GLU J 136 " --> pdb=" O SER J 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE J 139 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR J 140 " --> pdb=" O ASP J 137 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU J 150 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 108 removed outlier: 3.834A pdb=" N LEU K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 130 Processing helix chain 'K' and resid 132 through 165 removed outlier: 5.560A pdb=" N GLU K 136 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP K 137 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 106 Processing helix chain 'L' and resid 113 through 130 Processing helix chain 'L' and resid 132 through 162 removed outlier: 5.615A pdb=" N GLU L 136 " --> pdb=" O SER L 133 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE L 139 " --> pdb=" O GLU L 136 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET L 146 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU L 149 " --> pdb=" O MET L 146 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU L 150 " --> pdb=" O GLY L 147 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY L 153 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE L 155 " --> pdb=" O LEU L 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 130 removed outlier: 3.779A pdb=" N SER M 102 " --> pdb=" O ALA M 99 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER M 126 " --> pdb=" O ALA M 123 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR M 128 " --> pdb=" O VAL M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 165 Processing helix chain 'N' and resid 98 through 130 removed outlier: 3.817A pdb=" N MET N 108 " --> pdb=" O ALA N 104 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER N 109 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL N 110 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY N 111 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY N 112 " --> pdb=" O MET N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 164 Processing helix chain 'O' and resid 98 through 130 removed outlier: 4.037A pdb=" N LEU O 107 " --> pdb=" O ALA O 103 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER O 109 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY O 111 " --> pdb=" O LEU O 107 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY O 112 " --> pdb=" O MET O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 164 removed outlier: 5.892A pdb=" N GLU O 136 " --> pdb=" O SER O 133 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE O 139 " --> pdb=" O GLU O 136 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU O 150 " --> pdb=" O GLY O 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 130 removed outlier: 4.341A pdb=" N MET P 108 " --> pdb=" O ALA P 104 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER P 109 " --> pdb=" O ILE P 105 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL P 110 " --> pdb=" O ALA P 106 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY P 111 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY P 116 " --> pdb=" O GLY P 112 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N SER P 119 " --> pdb=" O GLN P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 164 Processing helix chain 'Q' and resid 97 through 130 removed outlier: 3.567A pdb=" N LEU Q 101 " --> pdb=" O GLY Q 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA Q 104 " --> pdb=" O SER Q 100 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER Q 109 " --> pdb=" O ILE Q 105 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL Q 110 " --> pdb=" O ALA Q 106 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY Q 111 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY Q 112 " --> pdb=" O MET Q 108 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN Q 115 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY Q 116 " --> pdb=" O GLY Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 165 removed outlier: 5.511A pdb=" N GLU Q 136 " --> pdb=" O SER Q 133 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE Q 139 " --> pdb=" O GLU Q 136 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU Q 150 " --> pdb=" O GLY Q 147 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N MET Q 159 " --> pdb=" O CYS Q 156 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.361A pdb=" N GLY A 123 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N PHE A 93 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 82 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 147 through 150 removed outlier: 4.238A pdb=" N GLU A 176 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 218 through 220 Processing sheet with id= D, first strand: chain 'A' and resid 281 through 286 removed outlier: 6.816A pdb=" N CYS A 253 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL A 284 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 255 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA A 286 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA A 257 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 372 " --> pdb=" O CYS A 316 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE A 318 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 374 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N TYR A 320 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 376 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 138 through 140 removed outlier: 6.644A pdb=" N ARG E 91 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL E 85 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL E 125 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ALA E 114 " --> pdb=" O VAL E 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 218 through 220 Processing sheet with id= G, first strand: chain 'E' and resid 281 through 286 removed outlier: 9.507A pdb=" N THR E 282 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N CYS E 253 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N VAL E 284 " --> pdb=" O CYS E 253 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR E 255 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ALA E 286 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA E 257 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS E 315 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE E 254 " --> pdb=" O HIS E 315 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL E 317 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL E 256 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE E 319 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL E 258 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASP E 321 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER E 372 " --> pdb=" O CYS E 316 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE E 318 " --> pdb=" O SER E 372 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR E 374 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR E 320 " --> pdb=" O THR E 374 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU E 376 " --> pdb=" O TYR E 320 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 79 through 81 removed outlier: 6.435A pdb=" N GLY C 123 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE C 93 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL C 82 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 147 through 149 Processing sheet with id= J, first strand: chain 'C' and resid 401 through 404 removed outlier: 6.942A pdb=" N LEU C 217 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU C 404 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE C 219 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 281 through 286 removed outlier: 9.139A pdb=" N THR C 282 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS C 253 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL C 284 " --> pdb=" O CYS C 253 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR C 255 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ALA C 286 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA C 257 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS C 315 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE C 254 " --> pdb=" O HIS C 315 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL C 317 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL C 256 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 319 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL C 258 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP C 321 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 320 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 82 through 88 removed outlier: 6.769A pdb=" N ASP B 93 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL B 87 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 132 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL B 120 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS B 145 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 154 through 156 Processing sheet with id= N, first strand: chain 'B' and resid 410 through 413 removed outlier: 7.703A pdb=" N ILE B 223 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER B 385 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU B 225 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN B 387 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY B 227 " --> pdb=" O GLN B 387 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL B 389 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 330 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL B 386 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 332 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA B 388 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 334 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TYR B 390 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE B 251 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N PHE B 333 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 253 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ASP B 335 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 255 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA B 295 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY B 256 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 297 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 81 through 83 removed outlier: 6.720A pdb=" N ARG F 130 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS F 123 " --> pdb=" O THR F 128 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N THR F 128 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS F 95 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE F 84 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 154 through 156 Processing sheet with id= Q, first strand: chain 'F' and resid 410 through 413 removed outlier: 3.752A pdb=" N ALA F 410 " --> pdb=" O LYS F 222 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY F 224 " --> pdb=" O ALA F 410 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE F 223 " --> pdb=" O ILE F 383 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER F 385 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU F 225 " --> pdb=" O SER F 385 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN F 387 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL F 330 " --> pdb=" O THR F 384 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL F 386 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU F 332 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA F 388 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE F 334 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 295 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLY F 256 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL F 297 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY F 258 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY F 299 " --> pdb=" O GLY F 258 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 279 through 281 removed outlier: 3.696A pdb=" N LYS F 280 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.837A pdb=" N ARG D 130 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N HIS D 123 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS D 95 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE D 84 " --> pdb=" O HIS D 95 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 154 through 157 removed outlier: 4.368A pdb=" N LYS D 183 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 410 through 413 removed outlier: 7.712A pdb=" N ILE D 223 " --> pdb=" O ILE D 383 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER D 385 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU D 225 " --> pdb=" O SER D 385 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN D 387 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY D 227 " --> pdb=" O GLN D 387 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL D 389 " --> pdb=" O GLY D 227 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL D 330 " --> pdb=" O THR D 384 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL D 386 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU D 332 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA D 388 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE D 334 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N TYR D 390 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE D 251 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N PHE D 333 " --> pdb=" O PHE D 251 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 253 " --> pdb=" O PHE D 333 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP D 335 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA D 255 " --> pdb=" O ASP D 335 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA D 295 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLY D 256 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL D 297 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'g' and resid 207 through 215 removed outlier: 7.033A pdb=" N ASP g 209 " --> pdb=" O PHE g 202 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE g 202 " --> pdb=" O ASP g 209 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU g 211 " --> pdb=" O ASN g 200 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN g 200 " --> pdb=" O LEU g 211 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU g 213 " --> pdb=" O ILE g 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE g 198 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL g 215 " --> pdb=" O MET g 196 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N MET g 196 " --> pdb=" O VAL g 215 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASN g 200 " --> pdb=" O LEU g 110 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY g 146 " --> pdb=" O LYS g 164 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE g 166 " --> pdb=" O GLY g 146 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'd' and resid 83 through 87 removed outlier: 3.786A pdb=" N GLY d 111 " --> pdb=" O LEU d 87 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ARG d 95 " --> pdb=" O ARG d 63 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL d 65 " --> pdb=" O ILE d 93 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE d 93 " --> pdb=" O VAL d 65 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'd' and resid 65 through 68 Processing sheet with id= Y, first strand: chain 'e' and resid 40 through 44 removed outlier: 3.829A pdb=" N THR e 52 " --> pdb=" O VAL e 44 " (cutoff:3.500A) 1553 hydrogen bonds defined for protein. 3816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.25 Time building geometry restraints manager: 42.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 32904 1.03 - 1.23: 47 1.23 - 1.42: 13082 1.42 - 1.62: 19496 1.62 - 1.81: 310 Bond restraints: 65839 Sorted by residual: bond pdb=" C1' ATP A 601 " pdb=" C2' ATP A 601 " ideal model delta sigma weight residual 1.531 1.299 0.232 1.20e-02 6.94e+03 3.74e+02 bond pdb=" C1' ATP E 601 " pdb=" C2' ATP E 601 " ideal model delta sigma weight residual 1.531 1.301 0.230 1.20e-02 6.94e+03 3.68e+02 bond pdb=" C1' ATP C 601 " pdb=" C2' ATP C 601 " ideal model delta sigma weight residual 1.531 1.301 0.230 1.20e-02 6.94e+03 3.67e+02 bond pdb=" C1' ATP A 601 " pdb=" O4' ATP A 601 " ideal model delta sigma weight residual 1.416 1.616 -0.200 1.30e-02 5.92e+03 2.37e+02 bond pdb=" C1' ATP E 601 " pdb=" O4' ATP E 601 " ideal model delta sigma weight residual 1.416 1.614 -0.198 1.30e-02 5.92e+03 2.32e+02 ... (remaining 65834 not shown) Histogram of bond angle deviations from ideal: 84.80 - 94.65: 3 94.65 - 104.50: 535 104.50 - 114.34: 83353 114.34 - 124.19: 31825 124.19 - 134.04: 3664 Bond angle restraints: 119380 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 122.37 17.50 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.19 16.68 1.00e+00 1.00e+00 2.78e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 123.49 16.38 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 123.47 13.36 1.00e+00 1.00e+00 1.78e+02 angle pdb=" PA ATP E 601 " pdb=" O3A ATP E 601 " pdb=" PB ATP E 601 " ideal model delta sigma weight residual 136.83 123.66 13.17 1.00e+00 1.00e+00 1.74e+02 ... (remaining 119375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.17: 29339 28.17 - 56.34: 1292 56.34 - 84.51: 107 84.51 - 112.68: 20 112.68 - 140.85: 4 Dihedral angle restraints: 30762 sinusoidal: 17213 harmonic: 13549 Sorted by residual: dihedral pdb=" CA ASP F 335 " pdb=" C ASP F 335 " pdb=" N ASN F 336 " pdb=" CA ASN F 336 " ideal model delta harmonic sigma weight residual 180.00 57.76 122.24 0 5.00e+00 4.00e-02 5.98e+02 dihedral pdb=" CA ASP D 335 " pdb=" C ASP D 335 " pdb=" N ASN D 336 " pdb=" CA ASN D 336 " ideal model delta harmonic sigma weight residual -180.00 -74.87 -105.13 0 5.00e+00 4.00e-02 4.42e+02 dihedral pdb=" CA ASP B 335 " pdb=" C ASP B 335 " pdb=" N ASN B 336 " pdb=" CA ASN B 336 " ideal model delta harmonic sigma weight residual -180.00 -74.95 -105.05 0 5.00e+00 4.00e-02 4.41e+02 ... (remaining 30759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 5224 0.352 - 0.704: 0 0.704 - 1.056: 0 1.056 - 1.408: 0 1.408 - 1.760: 1 Chirality restraints: 5225 Sorted by residual: chirality pdb=" CG LEU C 462 " pdb=" CB LEU C 462 " pdb=" CD1 LEU C 462 " pdb=" CD2 LEU C 462 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.74e+01 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C2' ATP E 601 " pdb=" C1' ATP E 601 " pdb=" C3' ATP E 601 " pdb=" O2' ATP E 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.40 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5222 not shown) Planarity restraints: 9797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 336 " -0.024 2.00e-02 2.50e+03 3.93e-02 2.31e+01 pdb=" CG ASN D 336 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN D 336 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 336 " -0.065 2.00e-02 2.50e+03 pdb="HD21 ASN D 336 " -0.002 2.00e-02 2.50e+03 pdb="HD22 ASN D 336 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 336 " 0.022 2.00e-02 2.50e+03 3.88e-02 2.25e+01 pdb=" CG ASN F 336 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN F 336 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN F 336 " 0.068 2.00e-02 2.50e+03 pdb="HD21 ASN F 336 " 0.001 2.00e-02 2.50e+03 pdb="HD22 ASN F 336 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 458 " -0.006 2.00e-02 2.50e+03 2.37e-02 1.69e+01 pdb=" CG PHE C 458 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 458 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 458 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE C 458 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE C 458 " -0.045 2.00e-02 2.50e+03 pdb=" CZ PHE C 458 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE C 458 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE C 458 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE C 458 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE C 458 " 0.043 2.00e-02 2.50e+03 pdb=" HZ PHE C 458 " 0.006 2.00e-02 2.50e+03 ... (remaining 9794 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1609 2.13 - 2.74: 124469 2.74 - 3.36: 183959 3.36 - 3.98: 239218 3.98 - 4.60: 393047 Nonbonded interactions: 942302 Sorted by model distance: nonbonded pdb=" OG SER D 348 " pdb="HH21 ARG D 353 " model vdw 1.507 1.850 nonbonded pdb=" O ALA C 388 " pdb=" HG1 THR C 392 " model vdw 1.546 1.850 nonbonded pdb=" O VAL J 157 " pdb=" HG SER J 160 " model vdw 1.565 1.850 nonbonded pdb=" H VAL A 158 " pdb=" OD2 ASP A 167 " model vdw 1.565 1.850 nonbonded pdb=" OE2 GLU i 68 " pdb=" H MET B 472 " model vdw 1.569 1.850 ... (remaining 942297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 78 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 79 through 564 or resid 601 through 602)) selection = chain 'C' selection = (chain 'E' and ((resid 78 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 79 through 226 or (resid 227 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name H or name \ HA or name HB or name HG21 or name HG22 or name HG23)) or resid 228 through 564 \ or resid 601 through 602)) } ncs_group { reference = (chain 'B' and ((resid 80 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD \ 21 or name HD22)) or resid 81 through 554)) selection = (chain 'D' and resid 80 through 554) selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.780 Extract box with map and model: 34.300 Check model and map are aligned: 0.770 Set scattering table: 0.500 Process input model: 162.560 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.232 32891 Z= 0.612 Angle : 0.697 17.503 44510 Z= 0.417 Chirality : 0.051 1.760 5225 Planarity : 0.004 0.059 5718 Dihedral : 14.548 140.847 12257 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.29 % Allowed : 1.74 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.12), residues: 4221 helix: -0.54 (0.11), residues: 2123 sheet: -1.60 (0.20), residues: 556 loop : -2.07 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 242 HIS 0.006 0.001 HIS F 112 PHE 0.027 0.002 PHE C 458 TYR 0.022 0.001 TYR D 185 ARG 0.005 0.000 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 763 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 753 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 TYR cc_start: 0.7566 (t80) cc_final: 0.6075 (t80) REVERT: C 102 GLU cc_start: 0.7946 (pt0) cc_final: 0.7742 (pt0) REVERT: C 462 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7665 (mp) REVERT: C 523 TYR cc_start: 0.7840 (t80) cc_final: 0.7288 (t80) REVERT: D 185 TYR cc_start: 0.8182 (m-10) cc_final: 0.7638 (m-10) REVERT: g 169 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7815 (mt-10) REVERT: g 219 THR cc_start: 0.8423 (p) cc_final: 0.7734 (m) REVERT: d 141 ASP cc_start: 0.6923 (t0) cc_final: 0.6388 (t0) REVERT: e 41 LYS cc_start: 0.8575 (tttt) cc_final: 0.8298 (tptt) REVERT: K 166 SER cc_start: 0.8251 (t) cc_final: 0.7965 (m) REVERT: L 159 MET cc_start: 0.7804 (mmp) cc_final: 0.7455 (mmm) REVERT: O 159 MET cc_start: 0.7006 (mmm) cc_final: 0.6659 (mmt) outliers start: 10 outliers final: 2 residues processed: 759 average time/residue: 1.0559 time to fit residues: 1186.7569 Evaluate side-chains 473 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 470 time to evaluate : 3.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain F residue 372 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 2.9990 chunk 318 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 329 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 200 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 381 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN E 121 ASN E 528 HIS C 223 GLN C 525 ASN C 529 GLN B 464 GLN D 242 ASN D 361 GLN g 261 ASN e 36 ASN e 47 GLN G 92 GLN M 131 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32891 Z= 0.214 Angle : 0.525 10.055 44510 Z= 0.273 Chirality : 0.047 1.775 5225 Planarity : 0.004 0.053 5718 Dihedral : 7.264 147.690 4712 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 0.99 % Allowed : 7.45 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 4221 helix: 0.20 (0.11), residues: 2134 sheet: -1.15 (0.21), residues: 554 loop : -1.38 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP g 242 HIS 0.004 0.001 HIS D 269 PHE 0.013 0.001 PHE i 73 TYR 0.021 0.001 TYR A 523 ARG 0.008 0.000 ARG F 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 538 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 504 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 75 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7825 (mtmt) REVERT: A 433 LYS cc_start: 0.7274 (mmmt) cc_final: 0.6910 (tptt) REVERT: C 523 TYR cc_start: 0.7505 (t80) cc_final: 0.7232 (t80) REVERT: F 238 MET cc_start: 0.8596 (mtt) cc_final: 0.8373 (mtt) REVERT: F 533 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: g 169 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7764 (mt-10) REVERT: G 94 GLU cc_start: 0.7014 (pm20) cc_final: 0.6787 (pm20) REVERT: K 166 SER cc_start: 0.8133 (t) cc_final: 0.7856 (m) REVERT: L 159 MET cc_start: 0.7854 (mmp) cc_final: 0.7439 (mmm) REVERT: O 159 MET cc_start: 0.7075 (mmm) cc_final: 0.6731 (mmt) REVERT: P 130 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7432 (mtp85) outliers start: 34 outliers final: 27 residues processed: 521 average time/residue: 1.0289 time to fit residues: 814.7856 Evaluate side-chains 471 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 443 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain g residue 65 MET Chi-restraints excluded: chain g residue 149 ASP Chi-restraints excluded: chain g residue 190 ASP Chi-restraints excluded: chain g residue 240 ASP Chi-restraints excluded: chain g residue 270 MET Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain M residue 131 ASN Chi-restraints excluded: chain O residue 133 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 382 optimal weight: 0.9990 chunk 412 optimal weight: 0.8980 chunk 340 optimal weight: 2.9990 chunk 378 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN B 123 HIS D 242 ASN e 34 GLN H 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 32891 Z= 0.295 Angle : 0.528 10.005 44510 Z= 0.274 Chirality : 0.047 1.712 5225 Planarity : 0.004 0.048 5718 Dihedral : 6.908 129.225 4710 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.19 % Allowed : 8.96 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4221 helix: 0.55 (0.12), residues: 2121 sheet: -0.88 (0.21), residues: 565 loop : -1.07 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 242 HIS 0.004 0.001 HIS D 269 PHE 0.014 0.001 PHE i 73 TYR 0.011 0.001 TYR F 298 ARG 0.007 0.000 ARG F 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 527 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 486 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 75 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7893 (mtmt) REVERT: A 433 LYS cc_start: 0.7484 (mmmt) cc_final: 0.7092 (tptt) REVERT: E 221 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: C 523 TYR cc_start: 0.7667 (t80) cc_final: 0.7334 (t80) REVERT: g 76 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.7195 (ttm170) REVERT: K 166 SER cc_start: 0.8140 (t) cc_final: 0.7898 (m) REVERT: L 159 MET cc_start: 0.7850 (mmp) cc_final: 0.7444 (mmm) REVERT: O 159 MET cc_start: 0.7151 (mmm) cc_final: 0.6767 (mmt) REVERT: P 130 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7383 (mtp85) outliers start: 41 outliers final: 32 residues processed: 506 average time/residue: 1.0376 time to fit residues: 795.1246 Evaluate side-chains 480 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 447 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain g residue 149 ASP Chi-restraints excluded: chain g residue 190 ASP Chi-restraints excluded: chain g residue 240 ASP Chi-restraints excluded: chain g residue 270 MET Chi-restraints excluded: chain d residue 161 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain K residue 133 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 256 optimal weight: 0.6980 chunk 383 optimal weight: 4.9990 chunk 405 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 363 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 525 ASN C 529 GLN ** F 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN H 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 32891 Z= 0.199 Angle : 0.490 9.826 44510 Z= 0.254 Chirality : 0.046 1.674 5225 Planarity : 0.004 0.042 5718 Dihedral : 6.501 115.039 4710 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.42 % Allowed : 9.54 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 4221 helix: 0.80 (0.12), residues: 2131 sheet: -0.74 (0.21), residues: 567 loop : -0.80 (0.17), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 242 HIS 0.004 0.001 HIS D 269 PHE 0.013 0.001 PHE D 251 TYR 0.014 0.001 TYR G 97 ARG 0.005 0.000 ARG G 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 520 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 471 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 75 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7898 (mtmt) REVERT: A 433 LYS cc_start: 0.7479 (mmmt) cc_final: 0.7117 (tptt) REVERT: E 216 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: B 420 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6622 (mm-30) REVERT: g 86 THR cc_start: 0.8398 (m) cc_final: 0.8176 (p) REVERT: d 125 CYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6580 (m) REVERT: H 131 ASN cc_start: 0.8136 (t0) cc_final: 0.7878 (t0) REVERT: K 166 SER cc_start: 0.8146 (t) cc_final: 0.7880 (m) REVERT: L 159 MET cc_start: 0.7890 (mmp) cc_final: 0.7416 (mmm) REVERT: O 159 MET cc_start: 0.7154 (mmm) cc_final: 0.6800 (mmt) outliers start: 49 outliers final: 38 residues processed: 501 average time/residue: 1.0528 time to fit residues: 804.7397 Evaluate side-chains 480 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 440 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain g residue 65 MET Chi-restraints excluded: chain g residue 149 ASP Chi-restraints excluded: chain g residue 190 ASP Chi-restraints excluded: chain g residue 240 ASP Chi-restraints excluded: chain g residue 270 MET Chi-restraints excluded: chain d residue 125 CYS Chi-restraints excluded: chain d residue 161 ASP Chi-restraints excluded: chain e residue 14 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain J residue 137 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 280 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 364 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 527 ASN B 114 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN D 361 GLN g 200 ASN e 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32891 Z= 0.305 Angle : 0.521 9.865 44510 Z= 0.272 Chirality : 0.047 1.677 5225 Planarity : 0.004 0.041 5718 Dihedral : 6.567 107.185 4710 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.65 % Allowed : 10.30 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4221 helix: 0.84 (0.12), residues: 2142 sheet: -0.66 (0.21), residues: 579 loop : -0.74 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 242 HIS 0.004 0.001 HIS D 269 PHE 0.014 0.001 PHE i 73 TYR 0.013 0.001 TYR F 298 ARG 0.006 0.000 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 523 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 466 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 75 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7939 (mtmt) REVERT: A 433 LYS cc_start: 0.7655 (mmmt) cc_final: 0.7295 (tptt) REVERT: E 216 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: F 238 MET cc_start: 0.8474 (mtp) cc_final: 0.8260 (mtm) REVERT: g 80 ASN cc_start: 0.8376 (m-40) cc_final: 0.8159 (m-40) REVERT: g 86 THR cc_start: 0.8525 (m) cc_final: 0.8249 (p) REVERT: K 166 SER cc_start: 0.8142 (t) cc_final: 0.7850 (m) REVERT: L 159 MET cc_start: 0.7917 (mmp) cc_final: 0.7427 (mmm) REVERT: O 159 MET cc_start: 0.7168 (mmm) cc_final: 0.6775 (mmt) outliers start: 57 outliers final: 44 residues processed: 502 average time/residue: 1.0362 time to fit residues: 790.6330 Evaluate side-chains 482 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 437 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain g residue 190 ASP Chi-restraints excluded: chain g residue 240 ASP Chi-restraints excluded: chain d residue 125 CYS Chi-restraints excluded: chain d residue 161 ASP Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 14 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain O residue 133 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 0.9990 chunk 365 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 chunk 406 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32891 Z= 0.266 Angle : 0.510 9.805 44510 Z= 0.264 Chirality : 0.046 1.679 5225 Planarity : 0.004 0.057 5718 Dihedral : 6.501 102.808 4710 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.74 % Allowed : 11.19 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4221 helix: 0.93 (0.12), residues: 2139 sheet: -0.59 (0.21), residues: 579 loop : -0.68 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 242 HIS 0.004 0.001 HIS D 269 PHE 0.043 0.001 PHE I 139 TYR 0.016 0.001 TYR J 141 ARG 0.008 0.000 ARG F 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 523 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 463 time to evaluate : 4.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 75 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7928 (mtmt) REVERT: A 433 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7366 (tptt) REVERT: E 216 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: g 80 ASN cc_start: 0.8348 (m-40) cc_final: 0.8120 (m-40) REVERT: g 86 THR cc_start: 0.8571 (m) cc_final: 0.8268 (p) REVERT: g 223 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: K 166 SER cc_start: 0.8131 (t) cc_final: 0.7826 (m) REVERT: L 159 MET cc_start: 0.7942 (mmp) cc_final: 0.7496 (mmm) REVERT: O 159 MET cc_start: 0.7145 (mmm) cc_final: 0.6788 (mmt) outliers start: 60 outliers final: 46 residues processed: 499 average time/residue: 1.0349 time to fit residues: 784.7276 Evaluate side-chains 485 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 437 time to evaluate : 4.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain g residue 190 ASP Chi-restraints excluded: chain g residue 223 GLN Chi-restraints excluded: chain g residue 240 ASP Chi-restraints excluded: chain d residue 125 CYS Chi-restraints excluded: chain d residue 161 ASP Chi-restraints excluded: chain e residue 14 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain J residue 137 ASP Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain Q residue 133 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 342 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 404 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 32891 Z= 0.368 Angle : 0.552 9.893 44510 Z= 0.289 Chirality : 0.048 1.684 5225 Planarity : 0.004 0.065 5718 Dihedral : 6.735 105.669 4710 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.06 % Allowed : 11.40 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 4221 helix: 0.84 (0.12), residues: 2148 sheet: -0.53 (0.21), residues: 581 loop : -0.73 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 242 HIS 0.005 0.001 HIS D 269 PHE 0.054 0.002 PHE I 139 TYR 0.021 0.001 TYR e 28 ARG 0.008 0.000 ARG G 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 525 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 454 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 75 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7940 (mtmt) REVERT: A 433 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7557 (tptt) REVERT: A 461 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6770 (m-30) REVERT: E 216 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: F 481 LEU cc_start: 0.8697 (tp) cc_final: 0.8425 (tp) REVERT: g 80 ASN cc_start: 0.8370 (m-40) cc_final: 0.8135 (m-40) REVERT: g 223 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: H 141 TYR cc_start: 0.8715 (m-80) cc_final: 0.8506 (m-10) REVERT: K 166 SER cc_start: 0.8151 (t) cc_final: 0.7840 (m) REVERT: L 159 MET cc_start: 0.7939 (mmp) cc_final: 0.7505 (mmm) REVERT: O 159 MET cc_start: 0.7185 (mmm) cc_final: 0.6815 (mmt) outliers start: 71 outliers final: 58 residues processed: 501 average time/residue: 1.0087 time to fit residues: 766.3052 Evaluate side-chains 491 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 430 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 523 ILE Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain g residue 223 GLN Chi-restraints excluded: chain g residue 240 ASP Chi-restraints excluded: chain d residue 125 CYS Chi-restraints excluded: chain d residue 161 ASP Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 14 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain Q residue 133 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 257 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 318 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 32891 Z= 0.183 Angle : 0.494 9.761 44510 Z= 0.255 Chirality : 0.046 1.675 5225 Planarity : 0.004 0.056 5718 Dihedral : 6.430 95.045 4710 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.54 % Allowed : 12.50 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 4221 helix: 1.05 (0.12), residues: 2138 sheet: -0.45 (0.21), residues: 576 loop : -0.57 (0.17), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 242 HIS 0.004 0.000 HIS D 269 PHE 0.015 0.001 PHE d 41 TYR 0.024 0.001 TYR e 28 ARG 0.008 0.000 ARG F 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 499 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 446 time to evaluate : 4.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 75 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7937 (mtmm) REVERT: A 433 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7469 (tptt) REVERT: A 461 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: E 221 ASP cc_start: 0.7732 (m-30) cc_final: 0.7508 (m-30) REVERT: g 80 ASN cc_start: 0.8322 (m-40) cc_final: 0.8067 (m-40) REVERT: g 223 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: K 166 SER cc_start: 0.8139 (t) cc_final: 0.7845 (m) REVERT: L 159 MET cc_start: 0.7904 (mmp) cc_final: 0.7468 (mmm) REVERT: O 159 MET cc_start: 0.7145 (mmm) cc_final: 0.6828 (mmt) outliers start: 53 outliers final: 46 residues processed: 483 average time/residue: 1.0788 time to fit residues: 802.4441 Evaluate side-chains 484 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 436 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain g residue 190 ASP Chi-restraints excluded: chain g residue 223 GLN Chi-restraints excluded: chain g residue 240 ASP Chi-restraints excluded: chain d residue 125 CYS Chi-restraints excluded: chain d residue 161 ASP Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 14 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain Q residue 133 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 0.5980 chunk 387 optimal weight: 0.7980 chunk 353 optimal weight: 1.9990 chunk 377 optimal weight: 0.2980 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 340 optimal weight: 2.9990 chunk 356 optimal weight: 0.1980 chunk 375 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32891 Z= 0.157 Angle : 0.481 9.881 44510 Z= 0.247 Chirality : 0.045 1.677 5225 Planarity : 0.004 0.063 5718 Dihedral : 6.090 85.454 4710 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.10 % Allowed : 13.17 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 4221 helix: 1.23 (0.12), residues: 2137 sheet: -0.31 (0.21), residues: 569 loop : -0.44 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 242 HIS 0.004 0.000 HIS D 269 PHE 0.012 0.001 PHE L 121 TYR 0.022 0.001 TYR e 28 ARG 0.007 0.000 ARG F 491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 486 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 448 time to evaluate : 4.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 75 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7921 (mtmm) REVERT: A 425 ARG cc_start: 0.7683 (mtt90) cc_final: 0.7342 (mtp85) REVERT: A 433 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7453 (tptt) REVERT: g 80 ASN cc_start: 0.8262 (m-40) cc_final: 0.7959 (m-40) REVERT: g 223 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8273 (mp10) REVERT: e 46 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6926 (tp40) REVERT: K 166 SER cc_start: 0.8129 (t) cc_final: 0.7832 (m) REVERT: L 159 MET cc_start: 0.7924 (mmp) cc_final: 0.7486 (mmm) REVERT: O 159 MET cc_start: 0.7184 (mmm) cc_final: 0.6853 (mmt) outliers start: 38 outliers final: 34 residues processed: 474 average time/residue: 1.0152 time to fit residues: 727.8770 Evaluate side-chains 472 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 437 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain g residue 223 GLN Chi-restraints excluded: chain d residue 125 CYS Chi-restraints excluded: chain d residue 161 ASP Chi-restraints excluded: chain e residue 14 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain Q residue 133 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 1.9990 chunk 398 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 418 optimal weight: 3.9990 chunk 385 optimal weight: 7.9990 chunk 333 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 257 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32891 Z= 0.264 Angle : 0.511 9.951 44510 Z= 0.264 Chirality : 0.046 1.686 5225 Planarity : 0.004 0.067 5718 Dihedral : 6.313 89.655 4710 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.22 % Allowed : 13.08 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 4221 helix: 1.16 (0.12), residues: 2143 sheet: -0.29 (0.21), residues: 576 loop : -0.48 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 242 HIS 0.004 0.001 HIS D 269 PHE 0.016 0.001 PHE d 41 TYR 0.024 0.001 TYR e 28 ARG 0.010 0.000 ARG G 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 482 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 440 time to evaluate : 4.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 75 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7937 (mtmm) REVERT: A 433 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7520 (tptt) REVERT: g 80 ASN cc_start: 0.8265 (m-40) cc_final: 0.7965 (m-40) REVERT: g 223 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: K 166 SER cc_start: 0.8107 (t) cc_final: 0.7818 (m) REVERT: L 159 MET cc_start: 0.7943 (mmp) cc_final: 0.7504 (mmm) REVERT: O 159 MET cc_start: 0.7265 (mmm) cc_final: 0.6873 (mmt) outliers start: 42 outliers final: 40 residues processed: 468 average time/residue: 1.0597 time to fit residues: 754.3109 Evaluate side-chains 471 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 430 time to evaluate : 4.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 78 GLU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain E residue 508 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain g residue 190 ASP Chi-restraints excluded: chain g residue 223 GLN Chi-restraints excluded: chain d residue 125 CYS Chi-restraints excluded: chain d residue 161 ASP Chi-restraints excluded: chain e residue 14 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain Q residue 133 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 307 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 333 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 342 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.0070 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 46 GLN e 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.124266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.090766 restraints weight = 129024.828| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.91 r_work: 0.2831 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 32891 Z= 0.182 Angle : 0.487 9.782 44510 Z= 0.250 Chirality : 0.045 1.677 5225 Planarity : 0.004 0.054 5718 Dihedral : 6.144 82.117 4710 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.28 % Allowed : 13.11 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 4221 helix: 1.26 (0.12), residues: 2138 sheet: -0.22 (0.22), residues: 572 loop : -0.39 (0.17), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 242 HIS 0.003 0.000 HIS D 269 PHE 0.014 0.001 PHE d 41 TYR 0.019 0.001 TYR e 28 ARG 0.008 0.000 ARG G 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15457.05 seconds wall clock time: 267 minutes 26.55 seconds (16046.55 seconds total)